“特藏寒羊”群体遗传结构分析与选择信号的对比分析

doi:10.11843/j.issn.0366-6964.2024.07.012

摘要/Abstract

摘要：

旨在了解“特藏寒羊”群体遗传结构和优势性能的遗传来源，为配种方案和杂交利用提供依据，帮助组建特定性能的家系。本研究应用SNP 50K v3芯片对50只“特藏寒羊”(公羊18只，母羊32只)、24只特克塞尔羊(公母各半)和48只欧拉羊(藏系绵羊)(公羊20只，母羊28只)进行单核苷酸多态性(single nucleotide polymorphisim，SNPs)检测；使用Plink、GCTA和MegaX软件对“特藏寒羊”进行遗传结构分析；Tajima’D法对“特藏寒羊”、特克塞尔羊和欧拉羊(藏系绵羊)进行群体内基因组选择信号分析，将“特藏寒羊”的选择信号分别与特克赛尔羊和欧拉羊(藏系绵羊)的选择信号取交集进行GO和KEGG功能富集分析，找到可能影响“特藏寒羊”优势性能的亲本来源和相关基因。结果显示：“特藏寒羊”平均多态信息含量(PIC)为0.26±0.12，平均期望杂合度(He)为0.36±0.14，平均观测杂合度(Ho)为0.37±0.16，平均最小等位基因频率(MAF)为0.25±0.15，平均有效等位基因数(Ne)为1.59±0.07；ROHs长度主要分布在1~5 Mb，占比50.4%，长度20 Mb⁺的ROH占比9.52%，近交系数F_ROH中位数为0.085；遗传距离D值为0.152 7~0.349 1，平均遗传距离0.279 6；NJ聚类分析共划分5个家系，家系内个体分布不均；“特藏寒羊”与欧拉羊(藏系绵羊)交集信号定位的基因与免疫相关，包括原发性免疫缺陷、造血细胞系和T细胞受体信号通路；“特藏寒羊”与特克塞尔羊交集信号定位的基因与生物代谢相关。综上所述，“特藏寒羊”存在一定程度近交，需加强管理；欧拉羊(藏系绵羊)更影响“特藏寒羊”免疫功能，特克塞尔羊更影响“特藏寒羊”生长发育和肉质性状。

关键词: 群体遗传结构, 选择信号分析, 欧拉羊(藏系绵羊)

Abstract:

The aim of this study was to understand the genetic structure and the genetic source of the dominant performance of 'Tezanghan' sheep, to provide the basis for the breeding plan and cross utilization, and to help the formation of the specific performance in different families. In this study, sheep SNP 50K v3 chip was used to detect the single nucleotide polymorphism of 50 'Tezanghan' sheep (18 rams, 32 ewes), 24 Texel sheep (12 rams, 12 ewes) and 48 Euler Tibetan sheep (20 rams, 28 ewes).Plink, GCTA and MegaX softwares were used to analyze the genetic structure of 'Tezanghan' sheep; Tajima'D method was used to analyze the intragroup genome selection signals of 'Tezanghan' sheep, Texel sheep and Euler Tibetan sheep; The selection signals of 'Tezanghan' sheep were intersected with those of Texel sheep and Ola sheep (Tibetan sheep) respectively for GO and KEGG functional enrichment analysis which was aimed to find out the parental origin and related genes that may affect the dominant performance of 'Tezanghan' sheep. The results showed that the average polymorphism information content (PIC), the average expected heterozygosity (He), the average observed heterozygosity (Ho), the average effective allele number (Ne) and the average minimum allele frequency (MAF) of 'Tezanghan' sheep were 0.26±0.12, 0.36±0.14, 0.37±0.16, 1.59±0.07 and 0.25±0.15, respectively. The length of ROHs mainly distributed in 1-5 Mb, accounting for 50.4%, the length of 20 Mb⁺ ROH accounted for 9.52%, and the median F_ROH was 0.085. The D values of genetic distance ranged from 0.152 7 to 0.349 1, with an average genetic distance of 0.279 6. Five families were divided by NJ cluster analysis, and the distribution of individuals within the families was uneven. The localized genes according to intersected signals between 'Tezanghan' sheep and Euler Tibetan sheep were related to immunity, including primary immune deficiency, hematopoietic cell line and T cell receptor signaling pathway. The localized genes according to intersected signals between 'Tezanghan' sheep and Texel sheep were related to biological metabolism. In summary, 'Tezanghan' sheep had a certain degree of inbreeding, which indicated the needs of reinforced management; Euler Tibetan sheep had more influence on the immune function of 'Tezanghan' sheep, and Texel sheep more affected the growth and meat quality traits of 'Tezanghan' sheep.

Key words: population genetic structure, selective signals analysis, Euler Tibetan sheep

中图分类号:

S826.2

王婷, 张元庆, 闫益波, 上官明军, 郭宏宇, 王志武. “特藏寒羊”群体遗传结构分析与选择信号的对比分析[J]. 畜牧兽医学报, 2024, 55(7): 2913-2926.

Ting WANG, Yuanqing ZHANG, Yibo YAN, Mingjun SHANGGUAN, Hongyu GUO, Zhiwu WANG. The Genetic Structure Analysis and the Comparative Analysis of Selection Signals in 'Tezanghan' Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(7): 2913-2926.

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质量控制标准Quality control standard	SNPs标记数目Number of SNPs
标记总数Total number of SNPs	64 734
最小等位基因频率＜0.01的标记SNPs with MAF＜0.01	4 727
哈代-温伯格平衡检验P＜10^-6的标记SNPs with P＜10^-6 in Hardy-Weinberg equilibrium	88
SNP检出率＜0.90 SNPs with call rate＜0.90	1 158
X染色体上的标记SNPs on chromosome X	1 527
Y染色体上的标记SNPs on chromosome Y	1 251
插入/缺失Insertion/Deletion	9
通过质量控制的SNPs数SNPs used after quality control	55 974

类型Category	条目Item	基因数Count	P值P value
GO分析(生物学进程) GO (Biological process)	透明质酸代谢过程	3	0.001 2
	表皮生长因子受体信号转导途径	3	0.019 0
	房室管发育	2	0.035 0
	心包形态发生	2	0.035 0
	卵黄发生	2	0.035 0
GO分析(分子生物学功能) GO (Molecular biological function)	鸟苷酸核苷酸交换因子活性	8	0.001 1
	金属离子结合	18	0.040 0
	丝氨酸型内肽酶抑制剂活性	4	0.056 0
	蛋白-谷氨酰胺-γ-谷氨酰转移酶活性	2	0.063 0
KEGG通路分析 KEGG pathway	甲状腺激素合成	4	0.028 0
	原发性免疫缺陷	3	0.039 0
	造血细胞系	4	0.057 0
	T细胞受体信号通路	4	0.093 0

类型Category	条目Item	基因数Count	P值P value
GO分析(生物学进程) GO (Biological process)	Ras蛋白信号转导	4	0.001 8
	白细胞介素-12生成的正向调节	3	0.024 0
	色氨酸分解为犬尿氨酸的过程	2	0.037 0
	细胞内胆固醇转运	2	0.064 0
	赖氨酸羟基化	2	0.072 0
	CTP生物合成过程	2	0.072 0
	UTP生物合成过程	2	0.072 0
	GTP生物合成过程	2	0.081 0
	活化T细胞增殖的负调控	2	0.081 0
	蛋白质运输	5	0.098 0
GO分析(分子生物学功能) GO (Molecular biological function)	脂质结合	7	0.028 0
	吲哚胺2, 3-二加氧酶活性	2	0.038 0
	氨基酸跨膜转运体活性	2	0.039 0
	GDP结合	3	0.083 0
	磷脂酰肌醇3-激酶结合	2	0.092 0
	GTP酶活性	7	0.000 8
	GTP结合	8	0.019 0
KEGG通路分析 KEGG pathway	内分泌抵抗	5	0.047 0
	维生素消化和吸收	3	0.062 0
	自噬--动物	6	0.074 0
	ECM与受体的相互作用	4	0.077 0

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